I have not noticed a difference. If your batter is thick, that will help. When making brownies or a sheet cake, I sprinkle them on top and it works great. Also, the flour often shows through in the finished product if it's a chocolate cake.

I've read a bit about this and there are quite a few people who swear by tossing them in flour (first coating them very lightly in cooking spray so it sticks). As Susan mentioned below, sometimes, depending on the cake, the flour can show when it is baked. For this reason, in a chocolate cake, you can use cocoa powder instead of the flour. Personally, I try to use very thick batters to avoid the problem altogether. The reason coating the chips (or fruit/nuts) works (sort of) is because it creates a barrier between the batter and chip forming a little pocket for it to sit in and prevents sinking.